Hi @qcsciphi
Thanks for sharing your history.
The problem was probably introduced when creating the fasta input. I can’t see those details since the three files are in a different history, but you can review that step. It looks like two were from some original files, and the third had a replace function run on it.
So, I would suggest back tracking to those steps to see if anything odd was done by comparing the fasta content between the tutorial data and your custom data.
Keep in mind the data content as well. If you are changing the inputs to consider, you might need to adjust parameters in the workflow as well. As a guess, the error looks like the terms used with FeatureFinderMultiplex are not a match for your custom data (the fasta, or in one of the intermediate tools), and FFM died out not knowing what to do about the conflict. Since you have access to all the files and know your goals, maybe back track and make sure all the inputs and upstream steps make sense first, then experiment with changes directly in the history until it works, and finally adjust the workflow once you know exactly what to change.
I am running the workflow on the tutorial data in here to make sure that part is actually Ok. Not quite finished but did make it farther than yours so far. So, I don’t think the workflow itself is the overall root problem. This is more about the default template workflow not being quite a fit for your custom data inputs yet. Galaxy | Europe